


Enter the Red Queen

by Eff_Dragonkiller



Series: Impossible Things [2]
Category: Shadowhunters (TV)
Genre: 2021 Shadowhunters (TV) Rewatch, Alternate Universe, Discord: Malec Server, Discussion - Murder, Fraywood Brotp, Gen, Shadowhunter Culture & Customs
Language: English
Status: Completed
Published: 2021-01-16
Updated: 2021-01-16
Packaged: 2021-03-13 18:29:18
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 4,435
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28782732
Author URL: https://archiveofourown.org/users/Eff_Dragonkiller/pseuds/Eff_Dragonkiller
Summary: "Inquisitor Herondale to see you, Commander.""Thank you, Andrew." Alec dismissed him with a nod. His attention was on the bone beads placed among the Inquisitor's braids. This might be more difficult than he'd assumed. Almost twenty years and the woman was still in mourning for the family she lost to the Circle. “Madam Herondale, how can the New York Institute assist you today?"
Relationships: Alec Lightwood & Jace Wayland, Clary Fray & Alec Lightwood
Series: Impossible Things [2]
Series URL: https://archiveofourown.org/series/2098536
Comments: 22
Kudos: 134





	Enter the Red Queen

**Author's Note:**

> Many thanks to **Lyss** and **Kai** for helping me figure out where I was going with this! As well as everyone who enjoys the #runaway_prompts channel on the Malec Discord Server. I can't even pick apart how many ideas started there that have just infected this story. And finally to **lawsofchaos** who was gracious enough to let me steal a tiny bit of her worldbuilding. 
> 
> Happy reading!
> 
> ps. this is supposed to take the place of S1E2 - The Descent into Hell Isn't Easy.

Alec would be surprised to see his parabatai in his office at 7 o'clock in the morning, if he didn't think the man was just coming in from a late—unsanctioned—patrol. "Jace."

"Wisebern screwed up my security clearance again," the blond huffed, "Izzy and I both got harassed coming in from patrol."

Wisebern didn't make mistakes with security clearances. Wisebern rarely made mistakes at all.

"I'll talk to him about it." Alec settled behind his desk, tea mug on the coaster just like Ava nagged. "Have you filed your reports yet?"

"I thought I could give you a verbal report, like old times." Jace offered with a smirk.

"Jace," Alec sighed, "You need to fill out your own report."

"It's a waste of time."

"A waste of time?" Alec scowled at his brother, "You go through more armor and weapons than any other two Shadowhunters at the Institute. These reports don't just prove or disprove intelligence, they're used for inventory and scheduling. Seriously, Jace, a verbal report isn't going to cut it."

His brother frowned, "You don't normally hassle me about them."

"Yeah, because I'm the one most often with you, idiot. I dock your pay for failure to report on patrols and everyone who needs to, gets the information they need from my report."

Jace stared incredulously, "You dock my pay?"

Alec loved his brother, perhaps too much according to the Clave, but he really was an idiot. "It's on your paystub, Jace. It’s been consistently on your paystub for years."

"You could've told me."

"I shouldn't have to," Alec frowned. "You're an adult; you've been running missions for six years. It's literally part of intro training." Now there was a thought. "Unless you'd like me to dump you back in probationary training?"

Jace opened his mouth, scowl in place—ready to give a blistering rebuttal, Alec was sure—when there was a knock on his door.

"Come in."

"Hey, boss." Ella said bouncing in, a far less awake foundling trailing in her wake. "Just here to drop off Clary."

"Great," Alec pointed to the seat Jace had propped his feet up in, "Pull up a chair. We're going to be here awhile." He turned to his brother, "And you, unless you want your clearance revoked permanently, do your damn paperwork."

Jace scowled at him briefly, but his attention had turned back to Clary. Eyes lingering on her long red hair, the shape of her figure in the borrowed clothes. Something twinged in Alec’s chest. Jace wouldn’t even give him five minutes of his time without an argument over something, when he suddenly had so much free time for any woman who caught his eye.

Alec didn’t know what he would do if he had to sit there and watch Jace flirt for an hour; it probably wouldn’t be pleasant. It certainly hadn’t been the last couple of times he’d ended up out with his siblings.

"Well, now, haven't seen you around recently. New transfer?"

Clary gasped and scowled. Fearlessly, she reached out and whacked Jace on the shoulder. “You ass, you were at the club! You walked into me! You killed that woman!”

“Stop it.” Jace dodged her hand, “And that woman was a demon. Not actually a person. And I did go after you to explain. I guess I know why tracking didn’t work.” Jace offered Clary a smarmy smirk, “We could work on finding something better to use in the future, though.”

Clary leaned back from Jace and Alec had to laugh at the look on her face, clearly sharing her opinion on when that might happen. Which, by the looks of it, would be at the dawn of never.

"Enough, Jace." Alec laughed, “This is Clary Fray. She’s my new trainee and the Institute’s newest foundling. Stop flirting.”

"Oh, come on, Alec." Jace pouted, "I was just being nice."

He scoffed, "You don't have a nice bone in your body. Get out."

Alec was tempted to go around his desk and tip his brother out of his chair. It wasn’t like it’d be the first time. Thankfully, though, Jace climbed to his feet on his own. It didn’t look like he’d need to endure much more of his brother’s attempts at flirting.

"Clary, was it? Hopefully, I'll see you soon. And without Mr. No-Fun in tow." He gave a small wave of his fingers as he closed the door behind him.

“Don’t forget the damn reports!”

 _Angel,_ his brother could be an asshole.

"Who was that?" Clary asked with wide eyes, “Besides a complete creeper.”

"Jace Wayland, my parabatai." Alec chuckled at her mix of confusion and disgust. "Right. You don't know what parabatai means. That's a great lead into what we need to talk about."

"What's that?" Clary shifted uncomfortably, "And is there a chance I could run home to grab my own clothes?"

Alec grimaced, "I followed up on what your friend Simon said. Your home is gone, Clary. I'm sorry. There's probably not much to get even if we could."

He watched her swallow hard and blink back the tears at the realization. "Right, Simon said there was a fire."

"Likely set by your mother during her fight against the Circle." Alec nodded, "Investigations, that's Marina's Department, went over after the fire department was finished. Definitely a fight. There was residue from several Shadowhunters, a warlock, and later a demon. But it doesn't look like the demon stayed long. Likely pulled in by the angelic energy of the fight."

"Investigations—they're looking for my mom?"

Alec hesitated, he didn't honestly want to tell her. But he'd sworn an oath, and even the thought of holding the information back caused the rune to burn a little. "Yes, but it's complicated."

Clary scowled and opened her mouth, but paused. She looked around the room again and Alec didn't know what caught her attention, but when she turned back to him she took a deep breath and tried to remain calm. "Can you explain it to me?"

So Alec does, because honesty and cooperation worked both ways. He had to be able to give a little to expect the same. He explained that Marina was looking for Clary's mother primarily because the woman was still wanted for questioning for her activities as a member of the Circle. That they believe the most likely candidate for kidnapping her mother was Valentine Morgenstern. A terrorist formerly believed dead, charged with the death of hundreds of downworlders and Shadowhunters.

Clary wrung her hands, "That sounds bad."

"It is bad." Alec agreed, "but it's a problem for later. What you need to do now, is to focus on your training as a Shadowhunter."

"My mom is out there with a terrorist! She could be dead and you want me to focus on training!"

Alec bit back the first thing he wanted to say. It wasn't polite for all that it would have been true. And reminded himself that if he were in the same situation looking for his family, Alec wouldn't be anywhere near calm and accepting.

"Clary, you can't help with the investigation because you don't have the training." Alec pointed out, "And-" He wasn't quite sure how to word this. "Listen, Clary, the Clave isn't like the mundane world. People don't get judged independent of their family name. Our society is too small. Every action you take reflects on your family and every time someone judges you, they have to consider your entire family as well."

"What does that mean?"

"It means that the better you do in your training, the better your standing with the Clave. The better your standing with the Clave, the more likely they are to be merciful with your mother."

"That's wrong." Clary frowned, "Courts shouldn't work like that!"

"No, they shouldn't, but they do. And right now, that's to your advantage. The better impression you leave with the Clave, the better your mother's odds are."

She bit her lip, "So what? Study hard, obey the rules, and hopefully if my mother is found it will be enough?"

Alec nodded, "It's not good, and I understand that, Clary. But it's what you need to do. Can you?"

Clary nodded sharply, "For my mom. Where do I start?"

"With culture," Alec said as he circled around the desk with a handful of hair ties and pins. "Nephilim have this thing about hair. Can I fix your hair? We're going to meet with a clave representative at some point today."

Clary bit her lip but nodded. "Do the braids mean anything? Explain it to me?"

A frown creased Alec’s forehead as he focused on keeping the braid forming between his fingers neat. "It's a custom that dates back to the first Nephilim. We wear our hair long in peacetime, for celebrations, or in private amongst close friends and family. According to tradition, our hair should be our glory. Only to be cut from shame or war."

"But lots of people have short hair here." Clary pointed out, "Ella, um, Andrew? Jace-the-creeper."

"Right, well, the New York Institute is a military base at war." Alec frowned, "Cutting it is just easier and simpler for a lot of people—though if you look even Ella and Andrew have enough for a small braid, enough to slide the beads for denoting their position on. But tying it up is steeped in tradition. Style and method can show a lot about what someone’s background is and what they think their strongest skill is. It’s a bit too complicated to explain now, and you haven’t earned any beads, but with the Clave representative coming, I want all the advantages we can get."

"I get the feeling you're one of those people who's contingency plans have contingencies."

"There's nothing wrong with a good plan," Alec frowned.

A smile started in the corner of Clary's mouth and spread across her lips. "I bet you play chess, don't you? Plan the entire game out and all the options before you even make your first move."

"I don't play chess." He replied blandly, "And predicting what moves people will make sounds like a headache."

Clary squinted at him like she didn't believe him, but the oath rune wasn't burning. He didn't lie.

Alessio interrupted before Alec had to remind Clary of his promise, "Inquisitor Herondale is on her way in, Boss."

"Thanks, Ava."

Alec squeezed Clary’s shoulder gently, "Take a deep breath and remember that whatever happens next, I'll be right beside you."

The queasy-green look didn’t fade from Clary’s face, but it was the best he could do because within seconds the Institute’s Head of Security was knocking on the door and leading the Inquisitor in.

"Inquisitor Herondale to see you, Commander."

"Thank you, Andrew." Alec dismissed him with a nod. His attention was on the bone beads placed among the Inquisitor's braids. This might be more difficult than he'd assumed. Almost twenty years and the woman was still in mourning for the family she lost to the Circle. “Madam Herondale, how can the New York Institute assist you today?"

"You're lucky that report landed on my desk with my evening tea and not while I was out." Madam Herondale settled herself into the armchair in front of the desk with all the poise of a queen sitting on a throne. "Such sensitive information should never be allowed out of sight."

"I apologize," Alec said as he and Clary sat, "but I'm only an Acting Head. My ability to contact your office is limited."

"Indeed," The woman stared at him and Alec resisted the urge to pick a point behind her shoulder to gaze at. He was Acting Head of the New York Institute. He'd done the best he could with the resources at his disposal. "I was surprised the report was from you and not your parents."

"I considered the issue urgent. With my parents out of contact, I decided it couldn't wait." He paused for just a moment, the tension thick enough to cut with a knife. "Was I wrong?"

Ava quietly entered with a coffee service she gently placed on the edge of his desk and quickly served the three of them the hot beverage. Alec let the silence ride as his secretary left, taking a sip of his drink and enjoying the special blend Ava saved for important guests.

"No," the Inquisitor finally said, settling her cup back in its delicate saucer. "I can't say that this isn't an urgent matter." Putting her cup on the edge of the desk, the woman turned her attention on Clary. "You have Morgenstern's daughter, why isn't she locked in a cell, awaiting questioning?"

"There's nothing to question her on." Alec nodded at Madam Herondale's skeptical expression. "As I said in the report, Luke Garroway contacted the Institute concerning the resurgence of the Circle and confessed to being party to the suppression of Fray's angelic power and memories."

"You believe him?"

"There is evidence beyond his word," Alec shared, "Fray has none of the calluses and ticks of a trained Shadowhunter. Before receiving her first runes last night, she had none of the scars from stele use. She doesn't walk like a Shadowhunter, and she's completely clueless of anything of Shadowhunter society."

His guest considered Clary with a scowl, "She's still Morgenstern's daughter."

"It isn't the policy of the Clave to punish children for their parents' crimes." Alec pointed out delicately.

He was sharply reminded, as the Inquisitor turned her cutting attention on him, that policy was not just a concern for Clary now either. Alec hadn't had nearly enough time to come to terms with the allegations Garroway had made against his parents. Not nearly enough time.

"That's true," Imogen Herondale admitted at last. "Though, we must be careful as a society that we do not offer too many chances for bad growth. Sometimes even healthy growth should be pruned for the best possible future."

Alec didn't say anything but sipped his tea and tried to ignore the faint rattle of Clary's cup and saucer. "What can she offer to reassure you?"

"What do you intend to do with her?"

"It's my intention to put Clary through the Foundling program. It's designed for these kinds of situations."

"For the reappearance of a wanted couple's teenage daughter?"

"For introducing nephilim left outside the Clave's care to our mission and culture," Alec corrected delicately. Now she was just being obstructionist. "Jia Penhallow has reported success with her foundlings; I don't see why Clary won't succeed just as well. She has much more to motivate her."

"Oh?" The Inquisitor turned her attention to his foundling and raised a brow, "So keen on joining the Clave? Ready to swear your life to a higher calling?"

Alec wished he could have coached her in an answer, she'd gone milk pale at the direct question. But this was something she had to find her own truth to; Madam Herondale would not accept anything less.

"No, but I'm willing to learn." Clary said, wringing her hands. "I don't know much about the Clave, but a mission to protect the world from demons is definitely something I can support. And I trust Alec, he promised he would be as honest as possible in return for my cooperation."

"And your mother?" The woman asked, "you're not concerned about her?"

Clary shook her head, "I am concerned. I'm very concerned. But Alec's pointed out I don't have any of the training to help. And Luke was the one who told me to trust Alec. Alec said that a team from Investigations is looking for her."

"Yes. She is a wanted criminal."

"I understand that." Clary cringed, "I do. If my mother broke the law then she needs to face justice for it. Right now, I think I'm more worried because I don't know anything. She's just missing." She bowed her head, "Not knowing is the hardest part."

Something in that must have triggered some empathy in the Inquisitor, because from what Alec could tell, the woman seemed to soften just a bit.

"Not knowing is the hardest part," She sighed. "How do you intend to report her, Morgenstern or Fairchild?"

"I was going to file it under Fray." When the woman raised a brow, Alec continued, "both names are otherwise dead, and the only living members of either are wanted fugitives. I thought the protection of a new name and the potential for a new house was not unwarranted."

Madam Herondale stared at him, and Alec refused to fidget. "You intend to personally train her?"

"What better way to ensure she knows everything she should?"

She hummed, "And her memories? They could contain something of the Mortal Cup."

Alec nodded, "I plan to call the High Warlock, but the less this appears as something out of the ordinary, the better."

"I agree," The Inquisitor said finally, draining the last of her coffee and standing to her feet. Clary and Alec only an instant behind her. "I'll have my secretary send you the paperwork for Ms. Fray." She offered her hand after only a moment of consideration, "I look forward to your reports, Commander."

"Thank you, Madam Inquisitor." Brushing his fingers against the rune on his desk, "Ava, Madam Herondale is leaving."

"Yes, Boss."

"Is there anything else the New York Institute can do for you, Madam?"

"No," She said slowly, "but I'll be watching you, Lightwood. I'll be watching very carefully."

There wasn't much Alec could do with that, but offer a nod and see the woman out of his office.

"I get it now," Clary said as she slouched back into her seat. "What you said about needing all the advantages? That was terrifying."

Alec sighed, "Welcome to the Clave."

***

Alec stared at the files that littered the desk. He'd sworn he'd do his best to protect and guide Clary during her time in the Shadow World. Finding out that meant protecting her from his parents wasn't a surprise. He'd had to protect his younger siblings from his parents for years. Finding out it meant protecting her from half his Institute was something completely different.

"It cannot get out that Clary is the daughter of Valentine Morgenstern." Alec ordered his command team. "Until we can sort through this mess and find ways to neutralize the threat, no one else in the Institute can know."

"Except Valentine knows," Marina pointed out with a frown. "He could be hiring thugs, making deals with demons, or just offering an absolution for anyone who can bring his daughter to him. We can't control that."

"So we control what we can." Wisebern was a man younger than Alec by a month or so. And since his return from Tahiti, his usual smile had been absent entirely. Alec felt a little bad about that. "We limit people’s access, we investigate everyone, and we make it known that we have a no tolerance policy against Circle sympathizers."

"So that when we start transferring people out," Andrew tapped his stylus thoughtfully, "no one is surprised."

"Alright, confession time." Ella interrupted, hands waving. "I've got a list of about ten Shadowhunters I watch like a hawk already. And another ten I think are suspicious. I was just going to make them disappear quietly, but well, Marina told me I wasn't allowed to."

"You'd already killed nine others." The Head of Investigations said dryly, "I don't have enough time in the day to cover up all your crimes, Bridger."

Ella gasped, "That is an insult! I am perfectly capable of disposing of a body without evidence, thank you!"

Alec groaned, "Is that where that spike in Missing in Action came from? Angel damn it, Bridger! I spent weeks trying to figure out if someone was hunting Shadowhunters. Maryse practically started a new war accusing downworlders of murder!"

"Ah," Ella laughed nervously, "Oops?"

"Send me a briefing," Alec decided, "Otherwise, we're on a wartime footing against other nephilim and that's the reason for the lockdown. Is that the last of the agenda?"

Andrew coughed, a light flush spread over his cheeks. "We need to talk about Wayland."

"Okay," Alec sipped at his cold coffee to stall, but this discussion was never going to get any easier. "What's wrong with Jace?"

"Besides the fact that he refuses to properly sign out equipment?" Ian scowled.

"Or turn in his reports?" Marina scoffed.

"I had to ask for clarification four times on his report last month!" Ella agreed with a full-body flail.

Andrew grimaced, "He breaks the security cordon at night."

The room quieted at that, and Alec had to close his eyes to the sight of his leadership team. "This is why you revoked his access, Markus?"

"Yes." Alec wasn't looking, but he knew Wisebern and he could practically hear the other man grinding his teeth. "If we're at a wartime footing, against other nephilim with Shadowhunter training, we can't afford to overlook his negligence."

And it was negligence. It was vital that security protocol be followed to the letter, now more than ever. The Institute had too many members to know every face on sight. There were too many members to know each of them by the feel of their power brushing up against another's. Any demon could take the shape of a Shadowhunter, and if security protocols weren't being followed, the demon would be close enough to do serious damage before anyone noticed they didn't feel like one of them.

That was supposed to be what some of the wards on the Institute were for, but considering the New York Institute's wards were maintained by a warlock instead of the Angelic Core, Alec wasn't going to press his luck. Moreover, those wards were designed to keep demons out and mundanes ignorant. They weren't supposed to stop other Shadowhunters. And other Shadowhunters were exactly who their enemy was right now.

Alec gave a deep sigh. His heart ached, hurting his parabatai hurt him too. "Is Jace in any positions of leadership?"

"He's nominally Head of Field Operations," Markus said, "but Isaiah's been doing most of the work for weeks now."

"Officially demote Jace and give the position to Isaiah. Inform Jace..." Promoting Darkwater for Jace was an easy switch, but what could he do to punish his parabatai? Jace wasn't ever going to get anywhere if he didn't learn that there were rules that could not be broken. Alec wouldn’t always be there to cover his back. Some fights only one person could wage. "Inform Jace that he's being confined to the Institute for remedial training on security procedures. In fact," Alec let a small evil smile curl the corner of his mouth. "Inform my brother that he will not be released for field work until he is recertified on _all_ the current Clave procedures. Wisebern, can we test him on it somehow?"

"Already ahead of you, man." Wisebern smirked as he tapped out a note on his tablet. "We should make that a punishment detail for all rule breaking."

Ian huffed, "It'd probably work. Angel above, who wants to go through all those manuals again? Once was enough."

Alec figured that Jace's poor behavior was an example of how once was not enough, but he understood the point. The procedural documents were dry if nothing else.

"Is that all?"

"Until next week," Ian said, hurrying out. "When we all have to waste our time all over again."

"See you then, Whitehelm!" Ella called down the hall, a shit-eating smile on her face at the profanity that floated back to her. "He's always so easy!"

Alec shook his head. His command team were the best at what they did. It's just that sometimes what they didn't include being an adult. He considered checking in with Ava and then heading down to his sister's nest in medical with lunch. They hadn't spent much time together the last few days, except that one mission to Pandemonium. Which reminded him-

"Ava, who's the local High Warlock?"

"Magnus Bane, of Brooklyn, Boss."

"Can you send a fire message to his office? I'd like to meet with him to discuss something. Some time in the next week would be great, but leave the location up to him."

"Sure, Boss."

Someone stumbled into him, and without thinking Alec wrapped his arm around their shoulders. "Wow, are Shadowhunters up all hours?"

"Pretty much." Alec nodded, keeping hold of his trainee and steering her towards a bench just around the corner. From the way she practically fell into the seat, Darkwater must have had her working hard. "Demons aren't nocturnal, exactly, but they do come out predominantly at night. And trouble with werewolves and vampires generally happens at night as well."

"Hence the 24 hours, 7 days a week, always on military base." Clary nodded, "Makes sense. Do you have time for some culture questions? I read some stuff in the ' _So you've just found out you've got Angel blood_ ' packet and I'd like some examples."

Alec blinked, "Is that really what it's called?"

Clary giggled, "Yeah. Whoever wrote it had a really dry sense of humor."

"It came out of the LA Institute. They've always been... different." Alec cleared his throat, "How did things with Darkwater go?"

"He said I had good hand-eye coordination, but not enough strength for any of the standard weapons in the armory."

"That comes in time." Alec offered. "What is he planning to start you with?"

"Daggers, maybe?" She wrinkled her nose, "There’s two short-ish blades, come in a pair?"

Alec nodded. It wasn't a bad plan. It would take a while to build up Clary's endurance, but not as long as it would take to build up her strength. Daggers were lightweight and the style would take advantage of her size. It was a good choice.

"When's your next lesson?"

"Captain Darkwater has agreed to train me in the mornings on Monday, Wednesday, and Friday. Ella promised she'd work with me on hand to hand the other days of the week." Clary tipped her head back to look him in the eye, "But nothing is scheduled on Sundays. Do Shadowhunters do religion?"

"Not as such-"

Alec was interrupted as Andrew called his attention from across the Ops floor. His frown was enough to bring Alec striding over.

"It's Luke Garroway. He's on the steps of the Institute arguing with what sounds like a mundane." Andrew said, "They're catching a lot of people's attention."

Clary gasped and Alec turned to see her peering up at the monitor where the situation on their steps was being projected. "That's Simon!"

**Author's Note:**

> Two points I'd like to share with you: 
> 
> 1\. I was attempting to keep this on a weekly schedule. But that's not going to happen. I need more of a break between these fics than that. Otherwise I'm going to burn out. Which would not make any of us happy.
> 
> 2\. This is going to get dark. Really dark. Like wearing people's bones as jewelry dark (I actually already put that in, did anyone catch it?). I'm going to fill this series with the most interesting bits and bobs that I've seen and smush it all together into one cohesive pile of delightfulness. 
> 
> Those pieces are mostly dark and bitter, like the best chocolate, so this is your warning. If that's not your cup of tea, you might not want to continue with this series. 
> 
> Otherwise, friends, were going to cover quite a few delightful tropes.


End file.
